2026-09-23 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY audit_author citation citation_author em_admin em_author_list _audit_author.name _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author EXPERIMENTAL_SUMMARY citation citation_author em_admin em_author_list _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update RCSB RCSB 2025-01-13 2025-05-14 2025-05-14 2026-09-23 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM131860 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM047477 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM098399 United States Venette-Smith NL Vishwakarma RK Dollinger R Schultz J Venkatakrishnan V Babitzke P Anand G Gilmour DS Armache J-P Murakami KS polymerase, Pol II, transcription, mRNA Venette-Smith NL Vishwakarma RK Venkatakrishnan V Dollinger R Schultz J Babitzke P Anand G Gilmour DS Armache JP Murakami KS Nat Commun UK 17 2026 42711332 doi:10.1038/s41467-026-75963-0 2041-1723 EMD-48624 other EM volume

Structure of a native Drosophila melanogaster Pol II Elongation Complex

EMD-48622 other EM volume

Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk

EMD-48625 other EM volume

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Overall structure

EMD-48626 other EM volume

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

EMD-48619 other EM volume

Structure of a native Drosophila melanogaster octameric nucleosome

EMD-48620 other EM volume

Structure of a native Drosophila melanogaster hexameric nucleosome

EMD-48621 other EM volume

Structure of native Drosophila melanogaster DLST

9mu8 FULLOVERLAP EMDB EMD-48623 associated EM volume

Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk

EMDB EMD-48624 other EM volume

Structure of a native Drosophila melanogaster Pol II Elongation Complex

EMDB EMD-48622 other EM volume

Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk

EMDB EMD-48625 other EM volume

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Overall structure

EMDB EMD-48626 other EM volume

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

EMDB EMD-48619 other EM volume

Structure of a native Drosophila melanogaster octameric nucleosome

EMDB EMD-48620 other EM volume

Structure of a native Drosophila melanogaster hexameric nucleosome

EMDB EMD-48621 other EM volume

Structure of native Drosophila melanogaster DLST

PDB 9MU7 unspecified

Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk

PDB 9MU9 unspecified

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

PDB 9MU4 unspecified

Structure of a native Drosophila melanogaster octameric nucleosome

PDB 9MU5 unspecified

Structure of a native Drosophila melanogaster hexameric nucleosome

PDB 9MU6 unspecified

Structure of native Drosophila melanogaster DLST

Native purified Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk Native purified Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk 0 4 5 8 10 11 12 13

This entry represents a native Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk, obtained through stringent 3D classification and refinement.

Drosophila melanogaster 0.930 DNA-directed RNA polymerase II subunit RPB1 Drosophila melanogaster 0.16642037499999998 1 LEVO SKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDL AKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPD PNKKPGHGGCGHYQPSIRRTGLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLP VPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGK PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYP GAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNA DFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKM PQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLH ICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLR QTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDD YGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGED GLCGELVEFQNMPTVKLSNKSFEKRFKFDWSNERLMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQIFPNGE SKVVLPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKYV SEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKP KAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPTRISPWLLRI ELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLS DMTLQGIEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAV RKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGV SENIIMGQLPKMGTGCFDLLLDAEKCRFGI P04052 2.7.7.6 DNA-directed RNA polymerase II subunit RPB2 Drosophila melanogaster 0.132640062 1 LEVO ENAEEISHELWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQI YLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPVETQHQKTFIGKIPIMLRSTYCLLSQLTDRDL TELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSA IGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGARGARPGVT KDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNL MKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGR DGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNG CWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNY SWQVLVASGVVEYIDTLEEETVMIAMSPYDLKQDKDYAYCTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGK QAMGVYITNFHVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF YRSYKDSENKRVGDQEENFEKPHRGTCQGMRNAHYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKR DASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPH AIPSRMTIGHLIECLQGKLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQR LKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANL RNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVT P08266 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Drosophila melanogaster 0.030676198999999998 1 LEVO PYANQPSVQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFLAHRIGLIPLISDDVVER LQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELK LRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKFFFNVESAGALK PENIVVMGVQVLKNKLSNLQTQLSHESQN O97183 2.7.7.6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Drosophila melanogaster 0.00973651 1 LEVO GGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDWSIDEL IMVD Q24320 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Drosophila melanogaster 0.016946136999999997 1 LEVO AGVLFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDINSWLYPMELGDKFRLVLATTLREDGCPDSGEYNPMEHE GTRADSFEYVMYGKIYRIEGDEAHNEASRLSAYVSFGGLLMRLQGDANNLHGFEVDQHMYLLMKRLA Q9VNZ3 DNA-directed RNA polymerase II subunit RPB9 Drosophila melanogaster 0.013786585999999998 1 LEVO GFVGIRFCQECNNMLYPKEDKENKILLYACRNCDYKQEADSNCIYVNKIMHEIDELTHIVPDVISDPTLPRTEDHACPKC SHREAVFFQAQTRRAEEEMRLYYVCTNQNCTHRWTE P36958 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Drosophila melanogaster 0.007671124 1 LEVO MIIPIRCFTCGKVIGNKWESYLGLLQAEYTEGDALDALGLKRYCCRRMLLGHVDLIEKLLNYAPLEK Q9VC49 DNA-directed RNA polymerase II subunit RPB11 Drosophila melanogaster 0.01328824 1 LEVO MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQTTAD YSPQEAFMNAITDLLAELSLFEERFKDAIKEKKEGG Q9VJE4 DNA-directed RNA polymerase II subunit RPB12 Drosophila melanogaster 0.005647678 1 LEVO TAMTYICGECHHENEMRPRDPIRCRECGYRIMYKKRTKRLVVFDAR Q6IGE3 RNA Drosophila melanogaster 0.0032470999999999997 1 AAAAAAAAAA Template DNA Drosophila melanogaster 0.015134660999999999 1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) DNA Non-template DNA Drosophila melanogaster 0.012170104999999999 1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) DNA RPB5 homolog Drosophila melanogaster 0.024518331999999997 1 LEVO MDDEAETYKLWRIRKTIMQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIVLVAHNDDPTDQMFVFFPEEP KIGIKTIKTYCTRMQEENIHRAIVVVQGGMTPSAKQSLVDMAPKYILEQFLESELLINITEHELVPEHVVMTVEEKQELL SRYKLKENMLMRIQAGDPVARYFGLKRGQVVKIIRSSETAGRYISYRLVC Q7JZF5 ZINC ION 6.5409e-05 8 ZN singleParticle particle 1.0 7.5 150.0 NaCl Sodium chloride 10.0 HEPES-HCl HEPES 5.0 Glycerol Glycerol 1.0 EDTA EDTA 350.0 FLAG FLAG peptide

10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor

Quantifoil GOLD 200 GOLD HOLEY ETHANE 100 4 FEI VITROBOT MARK IV

double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes

TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 4 31103 50.65

Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360

1 2349308

Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (2,349,308) is the starting number of particles after initial cleanup and 3D classification of the data.

cryoSPARC 4.3.1

'Patch CTF Estimation' in cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 C1 BACK PROJECTION 3.37 FSC 0.143 CUT-OFF cryoSPARC 4.3.1 96409 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1

'Non-Uniform Refinement' in cryoSPARC

P04052 A AlphaFold in silico model P08266 B AlphaFold in silico model O97183 C AlphaFold in silico model Q9VEA5 D AlphaFold in silico model Q7JZF5 E AlphaFold in silico model Q24320 F AlphaFold in silico model Q9VFB5 G AlphaFold in silico model Q9VNZ3 H AlphaFold in silico model P36958 I AlphaFold in silico model Q9VC49 J AlphaFold in silico model Q9VJE4 K AlphaFold in silico model Q6IGE3 L AlphaFold in silico model AB INITIO MODEL

The model was based on PDB: 6GML. First, 6GML was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila melanogaster Pol II subunits were aligned to their 6GML counterparts, and further optimized in the density using rigid-body fit. For the final model optimization, phenix.real_space_refine was used

50.0 emd_48623_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.6943306 2.455401 0.006510156 0.052518763 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48623:::: Refined, auto-sharpened Coulomb potential density map with Bfactor = -51.7 emd_48623_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.68731856 2.1798215 0.0015117474 0.08325059 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48623:::: Half-map 1 emd_48623_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.6921389 1.9728547 0.0015196179 0.082759246 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48623:::: Half-map 2